Characterising Quantitative Spontaneous Retinal Venous Pulsations in Glaucoma

University of Technology Sydney. Graduate School of Health.Spontaneous retinal venous pulsations (SVPs) are a dynamic vascular marker for glaucoma but have been variably reported in people with glaucoma. However, current assessment methods pose limitations that render SVP detection unfeasible for glaucoma screening and assessment. This thesis explores the effectiveness of a novel tablet-based ophthalmoscope in detecting and quantifying SVPs in glaucoma. SVP amplitudes were extracted from fundus videos using a custom-written algorithm from 170 participants with a confirmed diagnosis of glaucoma or a glaucoma suspect. SVP’s association with established clinical structural and functional markers for glaucoma were assessed. SVPs were detected and quantified in all participants and were found to be comparable to standard structural markers for distinguishing confirmed glaucoma from glaucoma suspects cases. SVPs were found to differentiate different types of confirmed glaucoma as effectively as measures of intraocular pressure. The tablet-based ophthalmoscope overcomes many disadvantages of current SVP assessment techniques. As the detected SVPs are associated with early clinical markers of glaucoma, they may be used in the early detection of glaucoma and ongoing evaluation and management, potentially limiting glaucoma related vision loss. Further studies are required to determine whether longitudinal changes in SVPs reflect glaucomatous progression

A combined convolutional and recurrent neural network for enhanced glaucoma detection.

Glaucoma, a leading cause of blindness, is a multifaceted disease with several patho-physiological features manifesting in single fundus images (e.g., optic nerve cupping) as well as fundus videos (e.g., vascular pulsatility index). Current convolutional neural networks (CNNs) developed to detect glaucoma are all based on spatial features embedded in an image. We developed a combined CNN and recurrent neural network (RNN) that not only extracts the spatial features in a fundus image but also the temporal features embedded in a fundus video (i.e., sequential images). A total of 1810 fundus images and 295 fundus videos were used to train a CNN and a combined CNN and Long Short-Term Memory RNN. The combined CNN/RNN model reached an average F-measure of 96.2% in separating glaucoma from healthy eyes. In contrast, the base CNN model reached an average F-measure of only 79.2%. This proof-of-concept study demonstrates that extracting spatial and temporal features from fundus videos using a combined CNN and RNN, can markedly enhance the accuracy of glaucoma detection

Cognitive Performance on the Montreal Cognitive Assessment Test and Retinal Structural and Functional Measures in Glaucoma

Glaucoma, the leading cause of irreversible blindness, is classified as a neurodegenerative disease, and its incidence increases with age. Pathophysiological changes, such as the deposition of amyloid-beta plaques in the retinal ganglion cell layer, as well as neuropsychological changes, including cognitive decline, have been reported in glaucoma. However, the association between cognitive ability and retinal functional and structural measures in glaucoma, particularly glaucoma subtypes, has not been studied. We studied the association between cognitive ability and the visual field reliability indices as well as the retinal ganglion cell (RGC) count estimates in a cohort of glaucoma patients. Methods: A total of 95 eyes from 61 glaucoma patients were included. From these, 20 were normal-tension glaucoma (NTG), 25 were primary open-angle glaucoma (POAG), and 16 were glaucoma suspects. All the participants had a computerised Humphrey visual field (HVF) assessment and optical coherence tomography (OCT) scan and were administered the written Montreal Cognitive Assessment (MoCA) test. RGC count estimates were derived based on established formulas using the HVF and OCT results. A MoCA cut-off score of 25 and less was designated as cognitive impairment. Student’s t-test was used to assess differences between the groups. The Pearson correlation coefficient was used to assess the association between MoCA scores and retinal structural and functional measures. Results: Significant associations were found between MoCA scores and the false-negative and pattern standard deviation indices recorded on the HVF (r = −0.19, r = −0.22, p &lt; 0.05). The mean IOP was significantly lower in the cognitively impaired group (i.e., MOCA ≤ 25) (13.7 ± 3.6 vs. 15.7 ± 4.5, p &lt; 0.05). No significant association was found between RGC count estimates and MoCA scores. Analysis of these parameters in individual glaucoma subtypes did not reveal any group-specific significant associations either.</jats:p

RVD: A Handheld Device-Based Fundus Video Dataset for Retinal Vessel Segmentation

Retinal vessel segmentation is generally grounded in image-based datasets collected with bench-top devices. The static images naturally lose the dynamic characteristics of retina fluctuation, resulting in diminished dataset richness, and the usage of bench-top devices further restricts dataset scalability due to its limited accessibility. Considering these limitations, we introduce the first video-based retinal dataset by employing handheld devices for data acquisition. The dataset comprises 635 smartphone-based fundus videos collected from four different clinics, involving 415 patients from 50 to 75 years old. It delivers comprehensive and precise annotations of retinal structures in both spatial and temporal dimensions, aiming to advance the landscape of vasculature segmentation. Specifically, the dataset provides three levels of spatial annotations: binary vessel masks for overall retinal structure delineation, general vein-artery masks for distinguishing the vein and artery, and fine-grained vein-artery masks for further characterizing the granularities of each artery and vein. In addition, the dataset offers temporal annotations that capture the vessel pulsation characteristics, assisting in detecting ocular diseases that require fine-grained recognition of hemodynamic fluctuation. In application, our dataset exhibits a significant domain shift with respect to data captured by bench-top devices, thus posing great challenges to existing methods. In the experiments, we provide evaluation metrics and benchmark results on our dataset, reflecting both the potential and challenges it offers for vessel segmentation tasks. We hope this challenging dataset would significantly contribute to the development of eye disease diagnosis and early prevention

Evolutionarily conserved and non-conserved retrovirus restriction activities of artiodactyl APOBEC3F proteins

The APOBEC3 proteins are unique to mammals. Many inhibit retrovirus infection through a cDNA cytosine deamination mechanism. HIV-1 neutralizes this host defense through Vif, which triggers APOBEC3 ubiquitination and degradation. Here, we report an APOBEC3F-like, double deaminase domain protein from three artiodactyls: cattle, pigs and sheep. Like their human counterparts, APOBEC3F and APOBEC3G, the artiodactyl APOBEC3F proteins are DNA cytosine deaminases that locate predominantly to the cytosol and can inhibit the replication of HIV-1 and MLV. Retrovirus restriction is attributable to deaminase-dependent and -independent mechanisms, as deaminase-defective mutants retain significant anti-retroviral activity. However, unlike human APOBEC3F and APOBEC3G, the artiodactyl APOBEC3F proteins have an active N-terminal DNA cytosine deaminase domain, which elicits a broader dinucleotide deamination preference, and they are resistant to HIV-1 Vif. These data indicate that DNA cytosine deamination; sub-cellular localization and retrovirus restriction activities are conserved in mammals, whereas active site location, local mutational preferences and Vif susceptibility are not. Together, these studies indicate that some properties of the mammal-specific, APOBEC3-dependent retroelement restriction system are necessary and conserved, but others are simultaneously modular and highly adaptable

Metabolic and endocrine profiles and reproductive parameters in dairy cows under grazing conditions: effect of polymorphisms in somatotropic axis genes

<p>Abstract</p> <p>Background</p> <p>The present study hypothesized that GH-AluI and IGF-I-SnabI polymorphisms do change the metabolic/endocrine profiles in Holstein cows during the transition period, which in turn are associated with productive and reproductive parameters.</p> <p>Methods</p> <p>Holstein cows (Farm 1, primiparous cows, n = 110, and Farm 2, multiparous cows, n = 76) under grazing conditions were selected and GH and IGF-I genotypes were determined. Blood samples for metabolic/endocrine determinations were taken during the transition period and early lactation in both farms. Data was analyzed by farm using a repeated measures analyses including GH and IGF-I genotypes, days and interactions as fixed effects, sire and cow as random effects and calving date as covariate.</p> <p>Results and Discussion</p> <p>Frequencies of GH and IGF-I alleles were L:0.84, V:0.16 and A:0.60, B:0.40, respectively. The GH genotype was not associated with productive or reproductive variables, but interaction with days affected FCM yield in multiparous (farm 2) cows (LL yielded more than LV cows) in early lactation. The GH genotype affected NEFA and IGF-I concentrations in farm 1 (LV had higher NEFA and lower IGF-I than LL cows) suggesting a better energy status of LL cows.</p> <p>There was no effect of IGF-I genotype on productive variables, but a trend was found for FCM in farm 2 (AB cows yielded more than AA cows). IGF-I genotype affected calving first service interval in farm 1, and the interaction with days tended to affect FCM yield (AB cows had a shorter interval and yielded more FCM than BB cows). IGF-I genotype affected BHB, NEFA, and insulin concentrations in farm 1: primiparous BB cows had lower NEFA and BHB and higher insulin concentrations. In farm 2, there was no effect of IGF-I genotype, but there was an interaction with days on IGF-I concentration, suggesting a greater uncoupling somatropic axis in AB and BB than AA cows, being in accordance with greater FCM yield in AB cows.</p> <p>Conclusion</p> <p>The GH and IGF-I genotypes had no substantial effect on productive parameters, although IGF-I genotype affected calving-first service interval in primiparous cows. Besides, these genotypes may modify the endocrine/metabolic profiles of the transition dairy cow under grazing conditions.</p

Selection Signatures in Worldwide Sheep Populations

The diversity of populations in domestic species offers great opportunities to study genome response to selection. The recently published Sheep HapMap dataset is a great example of characterization of the world wide genetic diversity in sheep. In this study, we re-analyzed the Sheep HapMap dataset to identify selection signatures in worldwide sheep populations. Compared to previous analyses, we made use of statistical methods that (i) take account of the hierarchical structure of sheep populations, (ii) make use of linkage disequilibrium information and (iii) focus specifically on either recent or older selection signatures. We show that this allows pinpointing several new selection signatures in the sheep genome and distinguishing those related to modern breeding objectives and to earlier post-domestication constraints. The newly identified regions, together with the ones previously identified, reveal the extensive genome response to selection on morphology, color and adaptation to new environments